This is going to be a rather vague answer, but perhaps it helps.
Also, I'm speaking from experience, not knowledge - I did install different firmware and change the skin, and it worked.
But that doesn't mean it'll work every time for everyone.
From what I know, assuming that the firmware is like CoolEr/Kobo/probably most EB600 variants, most of the things you'd like to change cannot be changed.
That is, they are all built into the main program (which provides the GUI), and unless they made it changeable by use of external files, you'd have to recompile it - but you probably won't get the sources.
You could write your own main program and use that instead. But that's probably a lot of work.
Apparently there is an OpenInkpot version that runs on EB600 - but you need to check first if your EB600 is new enough. (My device is too old for example.)
Skin: easy to check - you have downloaded the firmware? See if there is a directory /skin inside the fs.tgz .
(I'd download and check myself, but I'm at work right now.)
While at it, check the /etc/init.d/rcS file to see if any backdoors are called. In the CoolEr for example there is this line, near the end:
Probably Netronix standard would be this line:
Which in turn would call a binary file on the SD card with this path: /mfg_test/mfg_test .
My KIDesign skin would use this file as well to install the new skin.
Bricking: Always possible. So be prepared for it.
As long as the firmware fits, it should be possible. I don't think there is much risk as long as you take firmware that you know works with your device.
(For example, if you know you have an EB600E, see if there is a fs.tgz file in the EB600E directory.)
Make sure you can access the SD card even without the eBook Reader. (I.e. don't use the reader to prepare the card. You can, but it's slow and if anything goes wrong you can't use the reader to prepare the restore-card.)
If you're willing to accept the risk, why not? If everything works as intended, you should be able to switch back, as long as you have the full firmware.